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Parents of autistic children led the drive to raise funds for the cause, anticipating the institute could become the premiere autism research institute in the world. Among the parents behind the institute are Chuck and Sarah Gardner, whose son Chas has been diagnosed with autism. Chuck is a Sacramento area building contractor and co-founder of the institute along with his wife, Sarah, a high-profile television anchorwoman in Sacramento.

The institute's largest contribution came from the California State Legislature, which provided $34 million to the institute for autism research. The efforts enabled construction of the institute's state-of-the-art facility at the UC Davis Medical Center campus in Sacramento. After the major funding from the State, Rick Rollens, the former Secretary of the California State Senate and one of the leaders in the effort to create the institute, said the National Institutes of Health (NIH) has only funded "the traditional, genetic-oriented research into autism. The M.I.N.D. Institute, having been established by parents concerned about the staggering implications of a possible autism epidemic, is demanding that scientists take research to the next level by looking at possible causes from different perspectives.

In October, 2002, the institute released a study appearing to confirm that the prevalence of autism has risen steeply. The study was led by Dr. Robert Byrd, whose team gathered information on 684 children with developmental disabilities from California's Department of Developmental Services regional centers. Byrd's team's reported autism was on the rise in California, and that the unprecedented increase is real and cannot be explained away by artificial factors such as misclassification and diagnostic criteria changes, nor by migration of children into California.

In 2006, the M.I.N.D. Institute launched its Autism Phenome Project, with the objective of identifying biological and behavioral patterns in order to define distinct autistic spectrum subtypes. According to Amaral, "Children with autism clearly are not all the same. The tremendous variation leads us to believe that autism is a group of disorders rather than a single disorder -- several autisms versus one autism."

1800 children, aged two to four years old, will be enrolled in the longitudinal study, 900 diagnosed with autism, 450 with developmental delays, and 450 neurotypical control subjects. The study will involve systematic analyses of immune systems, brain structures, genetics, environmental exposures and blood proteins and other developmental indicators, and the medical evaluations will continue for several years.